This documentation will help you to get started running the Encode WDL Pipelines. Continue reading based on what best describes your need:

  • Pipelines: Getting started to run a pipeline.
  • Developer: you want to develop an existing or create a new pipeline.

This is a supplementary work in progress for the official documentation that is hosted at the main wdl-pipelines page.

Getting Started

You will first set up required dependencies, and then proceed with the pipeline of your choice.

  • Setup all of the pipelines require Cromwell and Docker. Let’s set this up first.

After setup (which is brief for now) you can proceed by selecting a particular pipeline you want to run. Within these documentation bases are included instructions for running locally and with several cloud services. All options use Docker and Cromwell as a controller, so you should have already the minimum dependencies. Let’s go!


If you are a developer and want to contribute to a repository, you will need to clone it and set up your workspace accordingly.

  • 1. Prepare your Workspace: The first step is to clone a repository to your Github account, and download some sample data.
  • 2. Github Development: if you aren’t familiar with the Github flow to checkout branches for new features and changes.
  • 3. Get help If you need help, please don’t hesitate to reach out and we will help you!